Question: Codon Adaptation Index
gravatar for tigeradab
5.7 years ago by
tigeradab50 wrote:

How to choose a reference set of highly expressed genes for calculating Codon Adaptation Index? What if I do not have any experimental evidence related to their expression levels or on the other hand what if I have a newly annotated genome? Is it still possible to compute CAI?

codon genes index • 1.6k views
ADD COMMENTlink modified 5.7 years ago by 5heikki8.5k • written 5.7 years ago by tigeradab50
gravatar for 5heikki
5.7 years ago by
5heikki8.5k wrote:

Why do you think that highly expressed genes in particular would make a good CAI reference? Personally, I would go for a highly conserved (between taxa) set of genes.

ADD COMMENTlink written 5.7 years ago by 5heikki8.5k

Thanks for the reply. Yes. It might be a good idea if I want to see deviation of a coding sequence between taxa. But, in my case I would want to see the similarities between coding sequences within the same organism/taxon so as to find out genes which have some correlation like they are similarly expressed, or like they belong to same pathway, or they are functioning towards a defined biological objective, etc.

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by tigeradab50
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